Millennia ago, in the Antarctica, the Ancients depart.
In the modern day, Stargate Command has a base established in an Ancient outpost and are working to understand the technology and determine who has the gene necessary to control it. Daniel Jackson informs Dr Elizabeth Weir (the leader of the expedition) and Dr. Rodney McKay (the head scientist) that the symbols which could take them to Atlantis, which is somewhere in the Pegasus Galaxy, uses an eight-symbol Stargate address. Dr. Beckett (the expeditions head Surgeon), while reluctantly attempting to control the Ancient chair, sets off a 'drone' (an Ancient projectile weapon) that almost brings down Brigadier General O'Neill and pilot Major John Sheppard as they approach the base by helicopter.
O'Neill arrive and commends Sheppard on his exceptional flying and then Daniel briefs him on the discovery of the gate address and that they need the Z.P.M. to power the gate. Sheppard explores the base and stumbles upon Dr. Beckett at the control chair. Beckett explains to Sheppard, who has just been given security clearance, the chair device and how it have a certain gene to operate it. Sheppard proceeds to sit in the chair and activating it conforming the he has the gene. Dr. Weir offers him a spot on the expedition but he is a bit hesitant to go, which may very well be a one-way trip. O'Neill encourages him and, eventually, Sheppard agrees and joins in as everyone prepares for the expedition.
At Stargate Command the expedition prepares to leave and Sheppard meets Colonel Marshall Sumner (the military commander) and who is not too fond of Sheppard. Dr. Rodney McKay rigs the ZPM into the Stargate to provide the power necessary for an eight-symbol connection and they send a MALP through to ascertain conditions. The telemetry shows viable life support and they go through. Sumner and his men secure the gate area on the other side and begin exploring. They find a highly-advanced control room where all the systems activate when Sheppard approaches. Two scientist find a room full of small spacships and report to Weir. Sumner finds a window and discovers that they are in an underwater city and the ocean is being held back by a force field. Beckett finds a hologram of an Ancient woman who warns of a terrible enemy and explains that the city was sunk in a desperate attempt to save it. Fearing the siege would never end, she says, the Ancients used the Stargate to return to Earth. At this point, the scientists realize that power levels are dropping and it is determined the three main power cells (Z.P.M.s) are weakening.
Weir sends Sumner through the Ancients' Stargate (complete with iris-like force field) to start looking for a power source, or a safe haven in the Pegasus Galaxy. Sumner takes Sheppard, Lt. Ford, and a team through to a planet where they find humans living and they make friendly contact. They meet Teyla Emmagan, the leader of the Athosians, who warns them of the "Wraith".
The next day, Sumner and his men spot the ruins of what looks to have been a high-tech city. The Athosians advise them not to enter it, as local folklore warns it will bring the Wraith. While Sumner takes men into the city anyway, Teyla leads Sheppard to some local ruins that contain simple murals depicting the Wraith returning every few centuries to 'cull' the humans. While there, Sheppard finds a necklace that Teyla lost long ago and returns it to her.
As darkness again falls, the Stargate activates and three small spaceships come through. Sumner and his men prepare for the attack as the enemy closes in on the village.
(to be continued)